I'd really love it if Paladins' Lay on Hands and Clerics' Channel Energy were "convertable", so both could use the same Feats enabling alternate/secondary abilities, powered off Channel usages. This would give more 'play' to otherwise single-class Feats, yet feels "flavor appropriate" to me.
Likewise,
It'd be interesting if both of those Classes' Spell Progression worked in more sympathetic way:
If Paladin Casting was defined as equal to Cleric Casting of (Paladin Level /2) or (Paladin Level - X) level, a Cleric6/Paladin6 could have Caster Level AND SPELLS equivalent to a Cleric 8 or 9, for example (vs. a Single-Class Cleric 12, still a big difference). That would probably necessitate a change to the Spell Progression of Paladins (to match the formula for Cleric equivalency), but the outcome seems much more interesting. It'd also be interesting if Ranger/Druids and Sorcerors/Bards worked similarly (Spell Progression stacks; Class Abilities don't).
I know that a big goal of Pathfinder has been making SINGLE Class Characters more viable, and from what I've seen, it's accomplishing that goal (which I agree with) very well. That said, multi-class characters shouldn't have insurmountable penalties. I guess ultimately, I think the 2nd Edition approach to multi-classing was slightly better than 3rd Edition's - It's not really that Base-Class multiclass combos were over-powered in 3.x, but that PrC's and the like ended up stronger than single-class Base Classes.
Combining Martial Classes is much less problematic, because +X BAB and Feats/Abilities combine much better than overlapping Spell Progression (though certain Monsters could have specific "Martial Class Sympathy", e.g. Ogres: Barbarians, allowing them to qualify for Class Level-Dependent abilities?) This is one area where Casters DON'T work as well as "Melee", and I think Pathfinder could definitely improve this. I don't think we need to revert to 2nd Edition on this, but we can adjust things so the OUTCOME more closely matches what 2nd Edition achieved, at least for such "sympathetic" cases, as above.
I'm probably getting some-what off the "one topic per thread" you requested :-),
but I think a similar approach could apply to Monsters with SLAs (like Dragons) who take Class Levels. A Dragon with Caster Level 10, with 4 Levels of Sorceror/Wizard would thus have CL 14 and Spells equivalent to a CL 14 Dragon (which could be higher than simply advancing the Dragon 4 HD, for example, since Dragon HD don't correspond 1:1 to CL) Creatures with examples at various HD are easy to advance in this way, but the method could still be followed for those who don't come in all sizes: They simply add in new Spells/SLAs APPROPRIATE TO THE COMBINED CASTER LEVEL (instead of as a Sorceror 4, for example).
...otherwise, GREAT JOB SO FAR!!!!